NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
P62253 UniProt NPD GO	UB2G1_HUMAN	Ubiquitin-conjugating enzyme E2 G1 (EC 6.3.2.19) (Ubiquitin-protein ligase G1) (Ubiquitin carrier pr ...	0.12	-	nuc	0			601569	2AWF	169
P62254 UniProt NPD GO	UB2G1_MOUSE	Ubiquitin-conjugating enzyme E2 G1 (EC 6.3.2.19) (Ubiquitin-protein ligase G1) (Ubiquitin carrier pr ...	0.12	-	nuc	0					169
P62255 UniProt NPD GO	UB2G1_RAT	Ubiquitin-conjugating enzyme E2 G1 (EC 6.3.2.19) (Ubiquitin-protein ligase G1) (Ubiquitin carrier pr ...	0.12	-	nuc	0					169
Q2TA03 UniProt NPD GO	UB2J2_BOVIN	Ubiquitin-conjugating enzyme E2 J2 (EC 6.3.2.19)	0.12	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein (By simi ...				259
Q5R7J6 UniProt NPD GO	UBE2N_PONPY	Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19) (Ubiquitin-protein ligase N) (Ubiquitin carrier prot ...	0.12	-	mit	0					152
P61088 UniProt NPD GO	UBE2N_HUMAN	Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19) (Ubiquitin-protein ligase N) (Ubiquitin carrier prot ...	0.12	-	mit	0		cytoplasm [TAS] nucleus [IDA] UBC13-MMS2 complex [IDA]	603679	2C2V	152
P61089 UniProt NPD GO	UBE2N_MOUSE	Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19) (Ubiquitin-protein ligase N) (Ubiquitin carrier prot ...	0.12	-	mit	0		cytoplasm [ISS] nucleus [ISS] UBC13-MMS2 complex [ISS]			152
O19177 UniProt NPD GO	UN119_CANFA	Unc-119 protein homolog (Retinal protein 4) (CRG4) (Fragment)	0.12	-	cyt	0					95
Q9D428 UniProt NPD GO	CJ132_MOUSE	Uncharacterized protein C10orf132 homolog	0.12	-	nuc	0					167
Q8BH26 UniProt NPD GO	CN109_MOUSE	Uncharacterized protein C14orf109 homolog	0.12	-	cyt	2 *	Membrane; multi-pass membrane protein (Potential)				163
Q9H7T0 UniProt NPD GO	CN161_HUMAN	Uncharacterized protein C14orf161	0.12	-	cyt	1					638
Q4KM84 UniProt NPD GO	CA156_RAT	Uncharacterized protein C1orf156 homolog	0.12	-	cyt	0					362
Q9DA42 UniProt NPD GO	CT085_MOUSE	Uncharacterized protein C20orf85 homolog	0.12	-	nuc	0					136
Q3E833 UniProt NPD GO	PCC1_YEAST	Uncharacterized protein PCC1	0.12	-	cyt	0					88
P25654 UniProt NPD GO	YCY0_YEAST	Uncharacterized protein YCR090C	0.12	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			182
Q3E829 UniProt NPD GO	YD160_YEAST	Uncharacterized protein YDL160C-A	0.12	-	cyt	0					80
P53260 UniProt NPD GO	YG2R_YEAST	Uncharacterized protein YGR102C	0.12	-	cyt	0		mitochondrion [IDA]			183
Q12164 UniProt NPD GO	YL023_YEAST	Uncharacterized protein YLL023C	0.12	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			279
P53896 UniProt NPD GO	YNP8_YEAST	Uncharacterized protein YNL158W	0.12	-	end	2 *	Membrane; multi-pass membrane protein (Potential)	nuclear envelope [IDA]			198
P38776 UniProt NPD GO	YHK8_YEAST	Uncharacterized transporter YHR048W	0.12	-	end	12	Membrane; multi-pass membrane protein (Potential)				514
P56576 UniProt NPD GO	UH11_RAT	Unknown protein from 2D-PAGE of heart tissue (Spot P11) (Fragment)	0.12	-		0					7
P16163 UniProt NPD GO	URIC_DROME	Uricase (EC 1.7.3.3) (Urate oxidase)	0.12	-	mit	0	Peroxisome				352
P23194 UniProt NPD GO	URIC_DROVI	Uricase (EC 1.7.3.3) (Urate oxidase)	0.12	-	mit	0	Peroxisome				342
P11172 UniProt NPD GO	PYR5_HUMAN	Uridine 5'-monophosphate synthase (UMP synthase) [Includes: Orotate phosphoribosyltransferase (EC 2. ...	0.12	-	cyt	0			258900		480
Q9BT76 UniProt NPD GO	UPK3B_HUMAN	Uroplakin-3B precursor (Uroplakin IIIb) (UPIIIb) (p35)	0.12	-	mit	0	Membrane; single-pass type I membrane protein (Potential). Heterodimer formation with Uroplakin Ib i ...				320
P06132 UniProt NPD GO	DCUP_HUMAN	Uroporphyrinogen decarboxylase (EC 4.1.1.37) (URO-D) (UPD)	0.12	-	cyt	0	Cytoplasm		176100	1URO	367
Q5RDK5 UniProt NPD GO	DCUP_PONPY	Uroporphyrinogen decarboxylase (EC 4.1.1.37) (URO-D) (UPD)	0.12	-	cyt	0	Cytoplasm				367
P01145 UniProt NPD GO	UTS1_CATCO	Urotensin-1 (Urotensin I)	0.12	-	nuc	0	Secreted protein				41
Q765I2 UniProt NPD GO	UTS2B_RAT	Urotensin-2B precursor (Urotensin-IIB) (U-IIB) (UIIB) (Urotensin II-related peptide) (Urotensin 2 do ...	0.12	-	mit	0	Secreted protein				118
Q9LVM9 UniProt NPD GO	YKT62_ARATH	VAMP-like protein YKT62 (AtYKT62) (ATGP1-like protein)	0.12	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				199
Q01290 UniProt NPD GO	VPH1_NEUCR	Vacuolar ATP synthase 98 kDa subunit (Vacuolar ATPase 98 kDa subunit)	0.12	-	end	6	Vacuole; vacuolar membrane; multi-pass membrane protein				856
P38078 UniProt NPD GO	VATA_CANTR	Vacuolar ATP synthase catalytic subunit A (EC 3.6.3.14) (V-ATPase subunit A) [Contains: Endonuclease ...	0.12	-	nuc	0	Intracytoplasmic membrane. Membranes of various intracellular acidic compartments				1088
Q25691 UniProt NPD GO	VATB_PLAFA	Vacuolar ATP synthase subunit B (EC 3.6.3.14) (V-ATPase B subunit) (Vacuolar proton pump B subunit)	0.12	-	cyt	0					494
Q40078 UniProt NPD GO	VATB1_HORVU	Vacuolar ATP synthase subunit B isoform 1 (EC 3.6.3.14) (V-ATPase B subunit 1) (Vacuolar proton pump ...	0.12	-	cyt	0					488
P54641 UniProt NPD GO	VA0D_DICDI	Vacuolar ATP synthase subunit d (EC 3.6.3.14) (V-ATPase d subunit) (Vacuolar proton pump subunit d) ...	0.12	-	cyt	0					356
P93043 UniProt NPD GO	VPS41_ARATH	Vacuolar assembly protein VPS41 homolog	0.12	-	cyt	0					976
P93231 UniProt NPD GO	VPS41_LYCES	Vacuolar assembly protein VPS41 homolog	0.12	-	cyt	0					960
Q9T091 UniProt NPD GO	VPS26_ARATH	Vacuolar protein sorting 26 homolog (VPS26 protein homolog)	0.12	-	cyt	0					303
Q6AY86 UniProt NPD GO	VP26A_RAT	Vacuolar protein sorting 26A (Vesicle protein sorting 26A)	0.12	-	cyt	0	Cytoplasm. Endosome; endosomal membrane; peripheral membrane protein (By similarity)				327
P53285 UniProt NPD GO	VPS62_YEAST	Vacuolar protein sorting protein 62	0.12	-	mit	1 *					467
O97681 UniProt NPD GO	VPP2_BOVIN	Vacuolar proton translocating ATPase 116 kDa subunit A isoform 2 (V-ATPase 116 kDa isoform a2)	0.12	-	end	6	Membrane; multi-pass membrane protein				854
Q9CZ28 UniProt NPD GO	SNF8_MOUSE	Vacuolar sorting protein SNF8	0.12	-	mit	0	Cytoplasm (Probable). Nucleus (Probable)				258
Q96H20 UniProt NPD GO	SNF8_HUMAN	Vacuolar sorting protein SNF8 (ELL-associated protein of 30 kDa)	0.12	-	cyt	0	Cytoplasm (Probable). Nucleus (Probable)				258
P35779 UniProt NPD GO	VA3_SOLRI	Venom allergen 3 (Venom allergen III) (Allergen Sol r 3) (Sol r III)	0.12	-	nuc	0	Secreted protein. Venom reservoirs				211
P00985 UniProt NPD GO	IVBI2_HEMHA	Venom basic protease inhibitor 2	0.12	-	cyt	0	Secreted protein				57
P00986 UniProt NPD GO	IVBI2_NAJNI	Venom basic protease inhibitor 2 (Venom basic protease inhibitor II)	0.12	-	nuc	0	Secreted protein				57
P00990 UniProt NPD GO	IVBI2_DABRU	Venom basic protease inhibitor 2 (Venom basic protease inhibitor II) (RVV-II)	0.12	-	nuc	0	Secreted protein				60
P84013 UniProt NPD GO	TX22_PHOKE	Venom protein PKTx22C1 (Fragment)	0.12	-	nuc	0	Secreted protein				38
P84016 UniProt NPD GO	TX17_PHORI	Venom protein PRTx17C1	0.12	-	nuc	0	Secreted protein				32
O13060 UniProt NPD GO	VSPA_TRIGA	Venom serine proteinase 2A precursor (EC 3.4.21.-)	0.12	-	exc	0	Secreted protein				260

You are viewing entries 62101 to 62150 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.